I took a look at the scene and fixed it
1) your normals are reversed for the glass pot, you have the inside and outside of the pot flipped. I just selected all of the polygons and reversed them all
2) leave a small gap between then floor and glass pot
3) don't use glossy transparent for glass and water, unless you want that smoky type look - I changed them, but left the cauchy_B_coeff you had on - dispersion. That's why the glass has colours with it at 0.1

This really slows the render down though...
4) select all the polys of the glass pot and water object and optimise them to remove the normalising message in Indigo
5) I removed the phong tag on the water because the flat top was getting smoothing problems. Anything with a phong tag in Cindigo will get full smoothing. Looks bad on a flat surface..
6) you had the IOR swapped between the glass and water - glass = 1.5, water = 1.33
7) you didn't set any colour in the Indigo Material helper tag - the C4D colours won't be used when you render in Indigo